Part I: Systems Biology of the Cancer Genetic and Epigenetic Landscape 1. Detection of Combinatorial Mutational Patterns in Human Cancer Genomes by Exclusivity Analysis Hua Tan and Xiaobo Zhou 2. Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data Amanda J. Kedaigle and Ernest Fraenkel 3. Analyzing DNA Methylation Patterns during Tumor Evolution Heng Pan and Olivier Elemento 4. MicroRNA Networks in Breast Cancer Cells Andliena Tahiri, and Miriam R. Aure, and Vessela N. Kristensen 5.
Identifying Genetic Dependencies in Cancer by Analyzing siRNA Screens in Tumor Cell Line Panels James Campbell, Colm J. Ryan, and Christopher J. Lord Part II: Systems Analyses of Signaling Networks in Cancer Cells 6. Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells Jakob Wirbel, Pedro Cutillas, and Julio Saez-Rodriguez 7. Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research Stefka Tyanova and Juergen Cox 8. Quantitative Analysis of Tyrosine Kinase Signaling Across Differentially Embedded Human Glioblastoma Tumors Hannah Johnson and Forest M White 9. Prediction of Clinical Endpoints in Breast Cancer using NMR Metabolic Profiles Leslie R. Euceda, Tonje H.
Haukaas, Tone F. Bathen, and Guro F. Giskeødegård Part III: Systems Biology of Metastasis and Tumor/ Microenvironment Interactions 10. Stochastic and Deterministic Models for the Metastatic Emission Process: Formalisms and Crosslinks Christophe Gomez and Niklas Hartung 11. Mechanically Coupled Reaction-Diffusion Model to Predict Glioma Growth: Methodological Details David A. Hormuth II, Stephanie L. Eldridge, Jared A. Weis, Michael I.
Miga, and Thomas E. Yankeelov 12. Profiling Tumor Infiltrating Immune Cells with CIBERSORT Binbin Chen, Michael S. Khodadoust, Chih Long Liu, Aaron M. Newman, and Ash A. Alizadeh 13. Systems Biology Approaches in Cancer Pathology Aaron DeWard and Rebecca J. Critchley-Thorne Part IV: Modeling Drug Responses in Cancer Cells 14.
Bioinformatics Approaches to Predict Drug Responses from Genomic Sequencing Neel Madhukar and Olivier Elemento 15. A Robust Optimization Approach to Cancer Treatment under Toxicity Uncertainty Junfeng Zhu, Hamidreza Badri, and Kevin Leder 16. Modeling of Interactions between Cancer Stem Cells and their Microenvironment: Predicting Clinical Response Mary E. Sehl and Max S. Wicha 17. Methods for High-throughput Drug Combination Screening and Synergy Scoring Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio, and Jing Tang.